Implementing output for injects. Cleaning code

src/fpakc.f90

@@ -72,7 +72,7 @@ PROGRAM fpakc
     call boundariesEM_update()
 
     ! Update injects
-    call updateInjects
+    call updateInjects()
 
     !Checks if a species needs to me moved in this iteration
     CALL solver%updatePushSpecies()

src/modules/common/moduleRandom.f90

@@ -53,7 +53,7 @@ MODULE moduleRandom
       implicit none
 
       real(8):: rnd
-      real(8):: v1, v2, Rsquare
+      real(8):: v1, v2
 
       v1 = 0.d0
       do while (v1 <= 0.d0)

src/modules/init/moduleInput.f90

@@ -628,6 +628,7 @@ MODULE moduleInput
       USE moduleMesh
       USE moduleCaseParam
       USE moduleRefParam
+      use moduleOutput, only: collOutput
       USE OMP_LIB
       USE json_module
       IMPLICIT NONE
@@ -1426,50 +1427,17 @@ MODULE moduleInput
       CHARACTER(2):: iString
       CHARACTER(:), ALLOCATABLE:: object
       LOGICAL:: found
-      CHARACTER(:), ALLOCATABLE:: speciesName
-      CHARACTER(:), ALLOCATABLE:: name
-      REAL(8):: v
-      REAL(8), ALLOCATABLE:: temperature(:), normal(:)
-      REAL(8):: flow
-      CHARACTER(:), ALLOCATABLE:: units
-      character(:), allocatable:: type
-      INTEGER:: physicalSurface
-      INTEGER:: particlesPerEdge
-      INTEGER:: sp
 
       CALL config%info('inject', found, n_children = nInject)
-      ALLOCATE(inject(1:nInject))
+      ALLOCATE(injects(1:nInject))
       nPartInj = 0
       DO i = 1, nInject
         WRITE(iString, '(i2)') i
         object = 'inject(' // trim(iString) // ')'
 
-        !Find species
+        CALL initInject(injects(i)%obj, i, object, config)
-        CALL config%get(object // '.species', speciesName, found)
-        sp = speciesName2Index(speciesName)
 
-        CALL config%get(object // '.name',            name,            found)
+        CALL readVelDistr(config, injects(i)%obj, object)
-        CALL config%get(object // '.v',               v,               found)
-        CALL config%get(object // '.T',               temperature,     found)
-        CALL config%get(object // '.n',               normal,          found)
-        IF (.NOT. found) THEN
-          ALLOCATE(normal(1:3))
-          normal = 0.D0
-        END IF
-        CALL config%get(object // '.flow',            flow,            found)
-        CALL config%get(object // '.units',           units,           found)
-        CALL config%get(object // '.type',            type,            found)
-        if (.not. found) then
-          ! If no type is found, assume constant injection of particles
-          type = 'constant'
-        end if
-        CALL config%get(object // '.physicalSurface', physicalSurface, found)
-        particlesPerEdge = 0
-        CALL config%get(object // '.particlesPerEdge', particlesPerEdge, found)
-
-        CALL inject(i)%init(i, v, normal, temperature, flow, units, type, sp, physicalSurface, particlesPerEdge)
-
-        CALL readVelDistr(config, inject(i), object)
         
       END DO
 
@@ -1528,7 +1496,7 @@ MODULE moduleInput
       IMPLICIT NONE
 
       TYPE(json_file), INTENT(inout):: config
-      TYPE(injectGeneric), INTENT(inout):: inj
+      class(injectGeneric), INTENT(inout):: inj
       CHARACTER(:), ALLOCATABLE, INTENT(in):: object
       INTEGER:: i
       CHARACTER(2):: iString

src/modules/mesh/inout/text/moduleMeshOutputText.f90

@@ -1,9 +1,14 @@
 module moduleMeshOutputText
+  use moduleOutput, only: prefix,             &
+                          informFileCreation, &
+                          formatFileName,     &
+                          generateFilePath
+
   contains
 
     subroutine writeSpeciesOutput(self, fileID, speciesIndex)
       use moduleMesh
-      use moduleOutput
+      use moduleOutput, only: calculateOutput, outputFormat
       use moduleRefParam, only: L_ref
       implicit none
 
@@ -88,7 +93,6 @@ module moduleMeshOutputText
                                   speciesIndex)
 
       use moduleMesh
-      use moduleOutput
       use moduleAverage
       use moduleRefParam, only: L_ref
       implicit none
@@ -151,8 +155,8 @@ module moduleMeshOutputText
 
     subroutine printCollText(self)
       use moduleMesh
-      use moduleOutput
       use moduleCaseParam, only: timeStep
+      use moduleOutput, only: collOutput
       implicit none
       
       class(meshGeneric), intent(in):: self
@@ -190,6 +194,7 @@ module moduleMeshOutputText
     subroutine printEMText(self)
       use moduleMesh
       use moduleCaseParam, only: timeStep
+      use moduleOutput, only: emOutput
       implicit none
       
       class(meshParticles), intent(in):: self

src/modules/mesh/inout/vtu/moduleMeshOutputVTU.f90

@@ -1,9 +1,11 @@
 MODULE moduleMeshOutputVTU
+  use moduleOutput, only: prefix, informFileCreation, formatFileName, generateFilePath
 
   CONTAINS
 
     SUBROUTINE writeHeader(nNodes, nCells, fileID)
       USE moduleMesh
+      use moduleOutput, only: fmtInt
       IMPLICIT NONE
 
       INTEGER, INTENT(in):: nNodes, nCells
@@ -77,6 +79,7 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE writeMesh(self, fileID)
       USE moduleMesh
       USE moduleRefParam
+      use moduleOutput, only: fmtReal, fmtInt
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
@@ -159,6 +162,7 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE writeCollOutput(self,fileID)
       USE moduleMesh
       USE moduleCollisions
+      use moduleOutput, only: fmtInt
       IMPLICIT NONE
 
       CLASS(meshGeneric), INTENT(in):: self
@@ -185,6 +189,7 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE writeEM(self, fileID)
       USE moduleMesh
       USE moduleRefParam
+      use moduleOutput, only: fmtReal
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -381,6 +386,7 @@ MODULE moduleMeshOutputVTU
     SUBROUTINE printEMVTU(self)
       USE moduleMesh
       USE moduleCaseParam, ONLY: timeStep
+      use moduleOutput, only: emOutput
       IMPLICIT NONE
 
       CLASS(meshParticles), INTENT(in):: self
@@ -414,7 +420,6 @@ MODULE moduleMeshOutputVTU
 
     SUBROUTINE printAverageVTU(self)
       USE moduleMesh
-      use moduleOutput
       USE moduleSpecies
       IMPLICIT NONE
 

src/modules/mesh/moduleMesh.f90

@@ -1,7 +1,7 @@
 !moduleMesh: General module for Finite Element mesh
 MODULE moduleMesh
   USE moduleList
-  USE moduleOutput
+  USE moduleOutput, only: outputNode, emNode
   USE moduleCollisions
   use moduleSpecies, only: nSpecies
 

src/modules/mesh/moduleMesh@boundaryEM.f90

@@ -56,6 +56,7 @@ submodule(moduleMesh) boundaryEM
       use json_module
       use moduleRefParam, ONLY: Volt_ref, ti_ref
       use moduleErrors
+      use moduleOutput, only: path
       implicit none
 
       class(boundaryEMGeneric), allocatable, intent(inout):: self

src/modules/mesh/moduleMesh@boundaryParticle.f90

@@ -342,6 +342,7 @@ submodule(moduleMesh) boundaryParticle
 
     ! Print
     subroutine ionization_print(self, fileID)
+      use moduleOutput, only: fmtInt
       implicit none
 
       class(boundaryParticleGeneric), intent(inout):: self
@@ -473,6 +474,7 @@ submodule(moduleMesh) boundaryParticle
 
     ! Print output
     subroutine quasiNeutrality_print(self, fileID)
+      use moduleOutput, only: fmtColInt, fmtColReal
       implicit none
 
       class(boundaryParticleGeneric), intent(inout):: self
@@ -613,6 +615,7 @@ submodule(moduleMesh) boundaryParticle
 
     ! Print
     subroutine outflowAdaptive_print(self, fileID)
+      use moduleOutput, only: fmtColInt, fmtColReal
       implicit none
 
       class(boundaryParticleGeneric), intent(inout):: self
@@ -691,7 +694,12 @@ submodule(moduleMesh) boundaryParticle
     ! Writes the output into the Step_XXXXX_boundaryParticles file when the %print procedure is associated
     module subroutine boundariesParticle_write()
       use moduleCaseparam, only: timeStep
-      use moduleOutput, only:fileID_boundaryParticle, formatFileName, informFileCreation
+      use moduleOutput, only: fileID_boundaryParticle, &
+                              formatFileName, &
+                              informFileCreation,&
+                              boundaryParticleOutput,&
+                              generateFilePath, &
+                              prefix
       implicit none
 
       integer:: b
@@ -700,7 +708,7 @@ submodule(moduleMesh) boundaryParticle
       if (boundaryParticleOutput) then
         fileName = formatFileName(prefix, 'boundariesParticle', 'csv', timeStep)
         call informFileCreation(fileName)
-        open(fileID_boundaryParticle, file = path // folder // '/' //  fileName)
+        open(fileID_boundaryParticle, file = generateFilePath(fileName))
 
         do b = 1, nBoundariesParticle
           if (associated(boundariesParticle(b)%obj%print)) then

src/modules/moduleInject.f90

@@ -5,7 +5,7 @@ MODULE moduleInject
   use moduleMesh, only: meshEdgePointer
 
   !Generic injection of particles
-  TYPE:: injectGeneric
+  TYPE, abstract:: injectGeneric
     INTEGER:: id
     CHARACTER(:), ALLOCATABLE:: name
     REAL(8):: vMod !Velocity (module)
@@ -14,46 +14,130 @@ MODULE moduleInject
     LOGICAL:: fixDirection !The injection of particles has a fix direction defined by n
     INTEGER:: nParticles !Number of particles to introduce each time step
     CLASS(speciesGeneric), POINTER:: species !Species of injection
-    character(:), allocatable:: type
     INTEGER:: nEdges
     type(meshEdgePointer), allocatable:: edges(:)
     INTEGER, ALLOCATABLE:: particlesPerEdge(:) ! Particles per edge
     REAL(8), ALLOCATABLE:: weightPerEdge(:) ! Weight per edge
     REAL(8):: surface ! Total surface of injection
     TYPE(velDistCont):: v(1:3) !Velocity distribution function in each direction
+    procedure(updateInject_interface), pointer, pass:: update => null()
+    procedure(printInject_interface),  pointer, pass:: print  => null()
     CONTAINS
-      PROCEDURE, PASS:: init         => initInject
       PROCEDURE, PASS:: addParticles
 
   END TYPE injectGeneric
 
+  abstract interface
+    ! Update the values of the particle boundary model
+    subroutine updateInject_interface(self)
+      import injectGeneric
+
+      class(injectGeneric), intent(inout):: self
+
+    end subroutine updateInject_interface
+
+    ! Write the values of the particle boundary model
+    subroutine printInject_interface(self, fileID)
+      import injectGeneric
+
+      class(injectGeneric), intent(inout):: self
+      integer, intent(in):: fileID
+
+    end subroutine printInject_interface
+
+  end interface
+
+  ! Default type, constant inject of particles
+  type, extends(injectGeneric):: injectConstant
+
+  end type injectconstant
+
+  type, extends(injectGeneric):: injectQuasiNeutral
+
+  end type injectQuasiNeutral
+
+  ! Wrapper for injects
+  type:: injectWrapper
+    class(injectGeneric), allocatable:: obj
+
+  end type injectWrapper
+
   INTEGER:: nInject
-  TYPE(injectGeneric), ALLOCATABLE, target:: inject(:)
+  TYPE(injectWrapper), ALLOCATABLE, target:: injects(:)
 
   CONTAINS
     !Initialize an injection of particles
-    SUBROUTINE initInject(self, i, v, n, temperature, flow, units, type, sp, ps, particlesPerEdge)
+    SUBROUTINE initInject(self, i, object, config)
       USE moduleMesh
       USE moduleRefParam
       USE moduleConstParam
       USE moduleSpecies
       USE moduleSolver
       USE moduleErrors
+      use json_module
       IMPLICIT NONE
 
-      CLASS(injectGeneric), INTENT(inout):: self
+      CLASS(injectGeneric), allocatable, INTENT(inout):: self
       INTEGER, INTENT(in):: i
-      REAL(8), INTENT(in):: v, n(1:3), temperature(1:3)
+      character(:), allocatable, intent(in):: object
-      INTEGER, INTENT(in):: sp, ps, particlesPerEdge
+      type(json_file), intent(inout):: config
+      character(:), allocatable:: type
+      logical:: found
+      REAL(8):: v
+      real(8), allocatable:: n(:), temperature(:)
+      INTEGER:: sp, ps, particlesPerEdge
+      character(:), allocatable:: speciesName
       integer:: ps_index
       REAL(8):: tauInject
-      REAL(8), INTENT(in):: flow
+      REAL(8):: flow
-      CHARACTER(:), ALLOCATABLE, INTENT(in):: units
+      CHARACTER(:), ALLOCATABLE:: units
-      character(:), allocatable, intent(in):: type
       INTEGER:: e
       REAL(8):: fluxPerStep = 0.D0
 
+      !Type of injection
+      call config%get(object // '.type',            type,        found)
+      if (.not. found) then
+        ! If no type is found, assume constant injection of particles
+        type = 'constant'
+      end if
+
+      ! Assign type to inject and allocates it
+      select case(type)
+      case ('constant')
+        allocate(injectConstant:: self)
+
+      case ('quasiNeutral')
+        allocate(injectQuasiNeutral:: self)
+
+        self%update => updateQuasiNeutral
+
+      case default
+        call criticalError('No injection type ' // type // ' defined', 'initInject')
+      end select
+
       self%id =  i
+      call config%get(object // '.name',             self%name,        found)
+
+      !Find species
+      CALL config%get(object // '.species', speciesName, found)
+      sp = speciesName2Index(speciesName)
+
+      ! Velocity and direction of injection
+      call config%get(object // '.v',                v,                found)
+      call config%get(object // '.n',                n,                found)
+      if (.not. found) then
+        allocate(n(1:3))
+        n = 0.D0
+      end if
+      ! Temperature of injection
+      call config%get(object // '.T',                temperature,      found)
+      ! Flow
+      call config%get(object // '.flow',             flow,             found)
+      call config%get(object // '.units',            units,            found)
+      CALL config%get(object // '.physicalSurface',  ps,               found)
+      particlesPerEdge = 0
+      CALL config%get(object // '.particlesPerEdge', particlesPerEdge, found)
+
       self%vMod        =  v / v_ref
       self%n           =  n / NORM2(n)
       self%temperature =  temperature / T_ref
@@ -145,54 +229,31 @@ MODULE moduleInject
       !Scale particles for different species steps
       IF (self%nParticles == 0) CALL criticalError("The number of particles for inject is 0.", 'initInject')
 
-      ! Assign type to inject
-      select case(type)
-      case ('constant', 'quasiNeutral')
-        self%type = type
-      case default
-        call criticalError('No injection type ' // type // ' defined', 'initInject')
-      end select
-
     END SUBROUTINE initInject
 
-    !Injection of particles
-    SUBROUTINE doInjects()
-      USE moduleSpecies
-      USE moduleSolver
-      IMPLICIT NONE
-
-      INTEGER:: i
-      
-      !$OMP SINGLE
-      nPartInj = 0
-      DO i = 1, nInject
-        IF (solver%pusher(inject(i)%species%n)%pushSpecies) THEN 
-          nPartInj = nPartInj + inject(i)%nParticles
-
-        END IF
-
-      END DO
-
-      IF (ALLOCATED(partInj)) DEALLOCATE(partInj)
-      ALLOCATE(partInj(1:nPartInj))
-      !$OMP END SINGLE
-
-      DO i=1, nInject
-        IF (solver%pusher(inject(i)%species%n)%pushSpecies) THEN 
-          CALL inject(i)%addParticles()
-
-        END IF
-      END DO
-
-    END SUBROUTINE doInjects
-
     ! Update the value of injects
     subroutine updateInjects()
+      implicit none
+      
+      integer:: i
+
+      do i = 1, nInject
+        if (associated(injects(i)%obj%update)) then
+          call injects(i)%obj%update()
+
+        end if
+
+      end do
+
+    end subroutine updateInjects
+
+    ! Updates the flow in the injection to maintain quasineutrality
+    subroutine updateQuasiNeutral(self)
       use moduleMesh, only: meshEdge, meshNode, mesh, qSpecies
       implicit none
 
-      integer:: i, e, s, n
+      class(injectGeneric), intent(inout):: self
-      class(injectGeneric), pointer:: self
+      integer:: e, s, n
       integer, allocatable:: nodes(:)
       class(meshEdge), pointer:: edge
       real(8), allocatable:: density_nodes(:)
@@ -201,10 +262,8 @@ MODULE moduleInject
       real(8):: density_incident, density_rest
       real(8):: alpha
 
-      do i = 1, nInject
+      select type(self)
-        self => inject(i)
+      type is (injectQuasiNeutral)
-        select case(inject(i)%type)
-        case ('quasiNeutral')
         do e = 1, self%nEdges
           edge => self%edges(e)%obj
 
@@ -245,44 +304,47 @@ MODULE moduleInject
 
           end if
 
+          print *, e, alpha
+
           ! Adjust the weight of particles to match the new current
-            self%weightPerEdge(e) = self%weightPerEdge(e) + 1.0d-2 * alpha
+          self%weightPerEdge(e) = self%weightPerEdge(e) + 1.0d-1 * alpha
 
         end do
 
       end select
-      end do
 
-    end subroutine updateInjects
+    end subroutine updateQuasiNeutral
 
-    SUBROUTINE initVelDistMaxwellian(velDist, temperature, m)
+    !Injection of particles
+    SUBROUTINE doInjects()
+      USE moduleSpecies
+      USE moduleSolver
       IMPLICIT NONE
 
-      CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
+      INTEGER:: i
-      REAL(8), INTENT(in):: temperature, m
       
-      velDist = velDistMaxwellian(vTh = DSQRT(2.d0*temperature/m))
+      !$OMP SINGLE
+      nPartInj = 0
+      DO i = 1, nInject
+        IF (solver%pusher(injects(i)%obj%species%n)%pushSpecies) THEN 
+          nPartInj = nPartInj + injects(i)%obj%nParticles
 
-    END SUBROUTINE initVelDistMaxwellian
+        END IF
 
-    SUBROUTINE initVelDistHalfMaxwellian(velDist, temperature, m)
+      END DO
-      IMPLICIT NONE
 
-      CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
+      IF (ALLOCATED(partInj)) DEALLOCATE(partInj)
-      REAL(8), INTENT(in):: temperature, m
+      ALLOCATE(partInj(1:nPartInj))
+      !$OMP END SINGLE
 
-      velDist = velDistHalfMaxwellian(vTh = DSQRT(2.d0*temperature/m))
+      DO i=1, nInject
+        IF (solver%pusher(injects(i)%obj%species%n)%pushSpecies) THEN 
+          CALL injects(i)%obj%addParticles()
 
-    END SUBROUTINE initVelDistHalfMaxwellian
+        END IF
+      END DO
 
-    SUBROUTINE initVelDistDelta(velDist)
+    END SUBROUTINE doInjects
-      IMPLICIT NONE
-
-      CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
-
-      velDist = velDistDelta()
-
-    END SUBROUTINE initVelDistDelta
 
     !Add particles for the injection
     SUBROUTINE addParticles(self)
@@ -304,8 +366,8 @@ MODULE moduleInject
       !$OMP SINGLE
       nMin = 0
       DO i = 1, self%id -1
-        IF (solver%pusher(inject(i)%species%n)%pushSpecies) THEN 
+        IF (solver%pusher(injects(i)%obj%species%n)%pushSpecies) THEN 
-          nMin = nMin + inject(i)%nParticles
+          nMin = nMin + injects(i)%obj%nParticles
 
         END IF
 
@@ -381,4 +443,67 @@ MODULE moduleInject
 
     END SUBROUTINE addParticles
 
+    ! Writes the value of injects
+    subroutine writeInjects()
+      use moduleCaseparam, only: timeStep
+      use moduleOutput, only: fileID_inject, &
+                              formatFileName, &
+                              informFileCreation,&
+                              injectOutput,&
+                              generateFilePath, &
+                              prefix
+      implicit none
+      
+      integer:: i
+      character(:), allocatable:: fileName
+
+      if (injectOutput) then
+        fileName = formatFileName(prefix, 'injects', 'csv', timeStep)
+        call informFileCreation(fileName)
+        open(fileID_inject, file = generateFilePath(fileName))
+
+        do i = 1, nInject
+          if (associated(injects(i)%obj%print)) then
+            call injects(i)%obj%print(fileID_inject)
+
+          end if
+
+        end do
+
+        close(fileID_inject)
+
+      end if
+
+    end subroutine writeInjects
+
+    ! Inits for different velocity distribution functions
+    SUBROUTINE initVelDistMaxwellian(velDist, temperature, m)
+      IMPLICIT NONE
+
+      CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
+      REAL(8), INTENT(in):: temperature, m
+
+      velDist = velDistMaxwellian(vTh = DSQRT(2.d0*temperature/m))
+
+    END SUBROUTINE initVelDistMaxwellian
+
+    SUBROUTINE initVelDistHalfMaxwellian(velDist, temperature, m)
+      IMPLICIT NONE
+
+      CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
+      REAL(8), INTENT(in):: temperature, m
+
+      velDist = velDistHalfMaxwellian(vTh = DSQRT(2.d0*temperature/m))
+
+    END SUBROUTINE initVelDistHalfMaxwellian
+
+    SUBROUTINE initVelDistDelta(velDist)
+      IMPLICIT NONE
+
+      CLASS(velDistGeneric), ALLOCATABLE, INTENT(out):: velDist
+
+      velDist = velDistDelta()
+
+    END SUBROUTINE initVelDistDelta
+
 END MODULE moduleInject

src/modules/output/moduleOutput.f90

@@ -14,6 +14,7 @@ MODULE moduleOutput
   LOGICAL:: collOutput = .FALSE.
   LOGICAL:: emOutput   = .FALSE.
   logical:: boundaryParticleOutput = .false.
+  logical:: injectOutput = .false.
 
   ! Prefix for iteration files
   character(len=*), parameter:: prefix = 'Step'
@@ -33,6 +34,7 @@ MODULE moduleOutput
   integer, parameter:: fileID_output = 20           ! Base id for species/collisions/EM output
   integer, parameter:: fileID_boundaryParticle = 30 ! Particle boundaries
   integer, parameter:: fileID_boundaryEM = 31       ! EM boundaries
+  integer, parameter:: fileID_inject = 32          ! Injects
   integer, parameter:: fileID_reference = 40        ! Reference values
   integer, parameter:: fileID_time =50              ! Computation time